So this hack would work even if it was assembly? if I write in pure machine code, would this be avoidable?
If you write (and bootstrap!) a compiler yourself then there's no Thompson hack. But, as you are aware, you can't trust the hardware nowadays. Proprietary bootloaders and firmwares all the way down, loading unauditable binaries, doing things in your back. Modern CPU even have out-of-band management engines (a whole secondary computer with its CPU, OS and network access)
I wouldn't use Kolibri myself but I've been searching for a reasonably open small computer to run Linux. Something that -unlike the Raspberry Pi- can boot and, why not, use hardware graphics acceleration without binary blobs. If you've been looking into that yourself and have some findings to share... I think there are SoCs based on the Freescale i.MX6 platform with Vivante GPU that should fill the bill. Which one, I'm not sure. Keeping an eye on Risc-V boards too.
8-bit
You could buy a Commodore 64 and run LUnix on it. There's a TCP/IP stack, so you should be able to post a message in a textboard. https://en.wikipedia.org/wiki/LUnix
Necrocomputing is but a nice hobby. On the other hand, if you have $6000 to spend, the Talos II workstation is FSF-certified hardware: https://www.raptorcs.com/TALOSII/